--- a/MapRTTransformer.xml	Wed Mar 01 12:24:14 2017 -0500
+++ b/MapRTTransformer.xml	Wed Aug 09 09:08:09 2017 -0400
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
 <!--Proposed Tool Section: [Map Alignment]-->
-<tool id="MapRTTransformer" name="MapRTTransformer" version="2.1.0">
+<tool id="MapRTTransformer" name="MapRTTransformer" version="2.2.0">
   <description>Applies retention time transformations to maps.</description>
   <macros>
     <token name="@EXECUTABLE@">MapRTTransformer</token>
@@ -31,7 +31,12 @@
   -store_original_rt
 #end if
 #if $param_model_type:
-  -model:type $param_model_type
+  -model:type
+  #if " " in str($param_model_type):
+    "$param_model_type"
+  #else
+    $param_model_type
+  #end if
 #end if
 #if $param_model_linear_symmetric_regression:
   -model:linear:symmetric_regression
@@ -43,7 +48,12 @@
   -model:b_spline:num_nodes $param_model_b_spline_num_nodes
 #end if
 #if $param_model_b_spline_extrapolate:
-  -model:b_spline:extrapolate $param_model_b_spline_extrapolate
+  -model:b_spline:extrapolate
+  #if " " in str($param_model_b_spline_extrapolate):
+    "$param_model_b_spline_extrapolate"
+  #else
+    $param_model_b_spline_extrapolate
+  #end if
 #end if
 #if $param_model_b_spline_boundary_condition:
   -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
@@ -58,16 +68,36 @@
   -model:lowess:delta $param_model_lowess_delta
 #end if
 #if $param_model_lowess_interpolation_type:
-  -model:lowess:interpolation_type $param_model_lowess_interpolation_type
+  -model:lowess:interpolation_type
+  #if " " in str($param_model_lowess_interpolation_type):
+    "$param_model_lowess_interpolation_type"
+  #else
+    $param_model_lowess_interpolation_type
+  #end if
 #end if
 #if $param_model_lowess_extrapolation_type:
-  -model:lowess:extrapolation_type $param_model_lowess_extrapolation_type
+  -model:lowess:extrapolation_type
+  #if " " in str($param_model_lowess_extrapolation_type):
+    "$param_model_lowess_extrapolation_type"
+  #else
+    $param_model_lowess_extrapolation_type
+  #end if
 #end if
 #if $param_model_interpolated_interpolation_type:
-  -model:interpolated:interpolation_type $param_model_interpolated_interpolation_type
+  -model:interpolated:interpolation_type
+  #if " " in str($param_model_interpolated_interpolation_type):
+    "$param_model_interpolated_interpolation_type"
+  #else
+    $param_model_interpolated_interpolation_type
+  #end if
 #end if
 #if $param_model_interpolated_extrapolation_type:
-  -model:interpolated:extrapolation_type $param_model_interpolated_extrapolation_type
+  -model:interpolated:extrapolation_type
+  #if " " in str($param_model_interpolated_extrapolation_type):
+    "$param_model_interpolated_extrapolation_type"
+  #else
+    $param_model_interpolated_extrapolation_type
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
@@ -76,7 +106,7 @@
 #end if
 </command>
   <inputs>
-    <param name="param_in" type="data" format="featurexml,consensusxml,mzml,idxml" optional="True" label="Input file to transform (separated by blanks)" help="(-in) "/>
+    <param name="param_in" type="data" format="mzml,featurexml,consensusxml,idxml" optional="True" label="Input file to transform (separated by blanks)" help="(-in) "/>
     <param name="param_trafo_in" type="data" format="trafoxml" optional="False" label="Transformation to apply" help="(-trafo_in) "/>
     <param name="param_invert" display="radio" type="boolean" truevalue="-invert" falsevalue="" checked="false" optional="True" label="Invert transformation (approximatively) before applying it" help="(-invert) "/>
     <param name="param_store_original_rt" display="radio" type="boolean" truevalue="-store_original_rt" falsevalue="" checked="false" optional="True" label="Store the original retention times (before transformation) as meta data in the output file" help="(-store_original_rt) "/>